Rayan Cherki's 89th-minute strike snatched the points for Lyon, who had lost the lead just three minutes earlier to a Wissam Ben Yedder penalty.
Niko Kovac's Monaco have hauled themselves back into contention following a run of 13 wins in 16 matches since the start of the calendar year.
Ligue 1: Leonardo Balerdi, Alvaro Gonzalez on target as Marseille condemn Dijon to 11th defeat in a row
Leonardo Balerdi powered in a header at a corner in first-half stoppage time and Alvaro Gonzalez nodded in a second from another Dimitri Payet cross on 79 minutes.
European football matchday: Manchester City face upbeat West Ham; depleted Juventus travel to Hellas Verona
Manchester City holds a 10-point advantage over Manchester United and Leicester as the Premier League leader plays at a West Ham side unusually elevated in fourth place
As the game resumed, Neymar continued to complain before walking down the tunnel to the dressing room in the 57th minute.
The win moved Lorient off the bottom of the table and into 19th place and level on points with Dijon, which is 18th on goal difference.
Ligue 1: Lille move to top spot after holding PSG to goalless draw; Monaco snap losing run with 1-0 win over Dijon
Lille take first place in the French top flight from Lyon on goal difference after a match which saw just a handful of shots on target and very little in the way of incident.
Ligue 1: Kylian Mbappe scores penalty as PSG beat 10-man Lorient; Lille register easy win over Dijon
Mbappe's second-half penalty, when Andrew Gravillon was sent off, and Moise Kean's strike helped PSG to victory after Lille, who host the Champions League runners-up on Sunday, beat Dijon by the same scoreline.
Ligue 1: Moise Kean, Kylian Mbappe send PSG to top of table with win over Dijon; Lens-Nantes game called off amid COVID-19 cases
PSG were missing nine players due to injury or suspension, including Angel di Maria and Marco Verratti, while Mbappe was rested at kick-off ahead of a trip to Turkey to play Istanbul Basaksehir on Wednesday.
Alessandro Florenzi scored PSG's second on 77 minutes and Pablo Sarabia notched a fourth for the reigning champions as PSG climbed above Rennes on goal difference after a fifth successive win.
After Rennes defender Sacha Boey was sent off in the 35th minute for raising a foot near left back Reinildo's head, Lille took the lead five minutes later through forward Jonathan Bamba's low shot.
Kylian Mbappe capped a brilliant individual performance by scoring twice and creating another for Mauro Icardi as leaders Paris St Germain cruised to a comfortable 4-0 victory over Dijon in their Ligue 1 clash at the Parc des Princes
Champions League: PSG manager Thomas Tuchel defends change in team's system after defeat to Borussia Dortmund
PSG coach Thomas Tuchel defended a change in system against Borussia Dortmund despite a 2-1 loss in their Champions League Round of 16 first leg on Tuesday.
French Cup: Pablo Sarabia nets brace as Paris Saint-Germain complete thumping win over Dijon to seal semi-final spot
Paris Saint-Germain’s Pablo Sarabia scored twice as they swept past Dijon and into the semi-finals of the French Cup with a 6-1 thrashing on Wednesday.
Ligue 1: Marseille stay close to league leaders PSG with victory over Bordeaux; Stade Reims earn rare win Saint-Etienne
With its sixth consecutive league win, nine-time champion Marseille remained five points behind PSG, which has a game in hand.
Ligue 1: Reigning champions Paris Saint-Germain stunned by rock-bottom Dijon ahead of Club Brugge clash
Paris Saint-Germain suffered a shock 2-1 defeat at the hands of rock-bottom Dijon on Friday in a sapping setback to morale just days before they tackle Club Brugge in the Champions League.
Ligue 1: Marseille's sporadic run under Andre Villas-Boas continues with 1-1 draw at home against Rennes
The draw means Marseille are five points behind league leaders Paris Saint-Germain, who are two points ahead of Nantes and surprise package Angers
Ligue 1: Kylian Mbappe's 32nd goal helps PSG sign off season in style; Monaco ensure survival with win over Amiens
Monaco virtually made sure of their French Ligue 1 survival with a 2-0 win over Amiens on Saturday while champions PSG signed off their home campaign with Kylian Mbappe scoring his 32nd league goal of the season in a 4-0 win over Dijon.
Ligue 1: Amiens captain Prince Gouano halts match against Dijon to confront fans after alleged racial abuse
Friday's French Ligue 1 game between Dijon and Amiens was temporarily suspended after the visitors' captain Prince Gouano complained he was racially abused.
Ligue 1: Lyon's loss to struggling Dijon piles pressure on manager Bruno Genesio; AS Monaco inch towards safety
Lyon slipped to a second damaging defeat this week as a 3-1 loss to struggling Dijon and a hostile atmosphere at the Groupama Stadium piled the pressure on Bruno Genesio on Saturday.